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LRScaf: improving draft genomes using long noisy reads.

Mao Qin1, Shigang Wu1, Alun Li1

  • 1Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen, 518120, Guangdong, China.

BMC Genomics
|December 11, 2019
PubMed
Summary
This summary is machine-generated.

Long Reads Scaffolder (LRScaf) significantly improves genome assembly contiguity using long reads, offering a cost-effective solution for large genomes. It outperforms existing methods in speed and efficiency.

Keywords:
LRScafNanoporePacBioScaffolding algorithmThird generation sequencing technologies

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Third-generation sequencing (TGS) technologies offer potential for improving genome assembly.
  • Long reads from TGS can enhance fragmented draft assemblies from next-generation sequencing (NGS).
  • Existing scaffolding algorithms have limitations, especially for hybrid assembly on large genomes.

Purpose of the Study:

  • To develop and evaluate a scalable and efficient scaffolder, Long Reads Scaffolder (LRScaf), for improving genome assembly contiguity using long reads.
  • To comprehensively assess the performance of LRScaf against state-of-the-art scaffolders on diverse organisms.

Main Methods:

  • Development of the Long Reads Scaffolder (LRScaf) algorithm.
  • Performance evaluation across seven organisms: E. coli, S. cerevisiae, A. thaliana, O. sativa, S. pennellii, Z. mays, and H. sapiens.
  • Comparison with existing scaffolding tools using PacBio and Nanopore datasets.

Main Results:

  • LRScaf significantly boosts assembly contiguity, exemplified by substantial NGA50 increases in human datasets (CHM1 and NA12878).
  • LRScaf achieved the best NGA50 contiguity for A. thaliana, S. pennellii, Z. mays, and H. sapiens.
  • LRScaf demonstrated the shortest run time and practical RAM usage compared to other scaffolders.

Conclusions:

  • LRScaf provides superior or comparable scaffold contiguity and accuracy with the fastest run time among tested algorithms.
  • LRScaf offers a cost-effective method for enhancing the contiguity of draft assemblies, particularly for large genomes.